Legacy Of War
by D. Grey
Summary: My first attempt at Fan-fiction. Rated M for possible future content; violence and sexuality. An attempt to fit a more seriously flawed Shepard into the game. Please review and criticise; I haven't used a beta reader. Disclaimer: I don't own Mass Effect.
1. Chapter 1

The SSV Normandy, an innovative top-of-the-line alliance ship. Innovation frightened Shepard. The military was his entire life; he understood the need for innovation he would just rather have been serving on a mediocre 10 year old frigate watching Captain Anderson champion new ideas from afar. Shepard admired his commanding officer but he did not emulate the man.

Shepard waited on the crew deck, he looked through the crew manifest and held it in ambivalence; there was a fair number of stand-up officers such as Navigator Charles Pressly, but the crew not as carefully picked and a few stood out as dangerously unprofessional. He had already finished comprising a mental list of crewmen that he would soon have transferred and he only looked a second time as a means of excusing himself from any conversation a crewman might attempt to initiate.

The captain's voice over brought relief to a Shepard's desire for action: "Commander Shepard, suit up; we're approaching Eden Prime."

Shepard marched towards the bridge, the peculiar Turian design that the Normandy employed put the pilot too far forward and he had to weave his way past the bridge crew down a narrow walkway in order to meet with the ship's pilot.

The pilot was an annoying hot-headed little man who must have had more than a dozen strikes on his record for insubordination. He found the pilot arguing with a staff lieutenant about the council specialist, Nihilus, just as the man left. He paid no attention to what they were saying, assuming that the pilot, a Mister Moreau, was in the wrong.

He cut their discussion short "That's enough, you're soldiers; act like it!"

The reply came from the staff lieutenant "Sorry, Commander."

Shepard liked this man, he tried to recall his name; Alenko, Kaidan Alenko.

A few words from the captain gave Shepard his orders; report to the comm room. Before making his way into the room he intruded upon another argument.

A man by the name of Jenkins, a corporal, asked "What do you think, Commander? We won't be staying on Eden Prime too long, will we? I'm itching for some real action!"

This man's voice stank, his over-enthusiasm screamed liability, but before Shepard could chastise him the Chief Medical Officer retorted with an equally disturbing remark.

"I sincerely hope you're kidding, Corporal. You're 'real action' usual ends with me patching up crew members in the infirmary." This Dr. Chakwas sounded less the pleased to be doing the job she was paid to do.

"That is what your position entails, Doctor. Marines are meant to fight; you just patch us up when we're done."

Thankfully, the doctor did not challenge his authority. She continued to chide Jenkins, nonetheless, but he didn't get the message.

Shepard addressed the corporal, drawing on his air of authority, "Do your job; follow my orders and there won't be any problems."

Jenkins persisted "Easy for you to say; you proved yourself on Torfan, everyone knows what you can do…"

Shepard had had enough; he gave a harsh interruption "I don't like your tone, corporal. You will obey orders and if you do anything to screw this mission up you can be rest assured that you will never serve on an alliance ship again. Am I clear?"

The corporal murmured a reply but Shepard left for the comm room before he could hear his full apology.

Shepard had found Nihilus in the comm room, and assumed the Captain would arrive shortly. The Turian council agent, a member of a Special Forces group known as the spectres, had asked him about Eden Prime.

"…I've heard it's quite beautiful."

Shepard couldn't confirm this "I haven't been there, sir."

The word 'sir' had rolled so easily of the commander's tongue, he had been unsure of Nihilus' rank but the alien's tone had indicated authority and Shepard refused to test it.

Before long, the Captain had arrived and the true nature of the mission had been revealed. The mission to Eden Prime was more than a simple shake-down run; it was a covert pick up.

Ruins from a lost civilisation had been uncovered and, amongst them, a beacon of similar design to the Prothean technology that had brought humanity into the age of inter-stellar space flight needed to be taken to the Citadel, the centre of galactic society, for study.

This was not the only purpose of the mission, however, as Shepard had been selected as a candidate for the spectres, it was a chance for the council agent Nihilus to observe the commander and report as to his competence.

Shepard didn't like the idea of punching above his weight, but both Captain Anderson and Agent Nihilus demanded he take the opportunity and he would never refuse a request from two ranking officers.

Before their mission could begin however, the three were treated to an emergency distress signal from the planet's surface. The footage wasn't stable, but a battle could be clearly seen along with an unknown ship wreaking havoc with its local environment and the deaths of a number of human soldiers.

With adrenaline already starting to kick in, Shepard was immediately on-board with Nihilus' suggestion of sending a small strike team in to retrieve the beacon before this unseen enemy could.

The captain wasted no time "Tell Alenko and Jenkins to suit up, commander. You're going in!"


	2. Chapter 2

This mission had failed. Jenkins' inexperienced recklessness had cost him his life and Nihilus' self-assuredness had cost him his. They'd picked up survivor by the name of Ashley Williams; a gunnery chief just as hot-headed as Jenkins but with more combat experience.

Shepard had found someway to make their deaths his fault and nothing was going to change that.

He woke up on the Normandy's medical bay to the news, relayed to him by Doctor Chakwas and Chief Williams, that the beacon had also been destroyed as a result of Williams' inability to fall in line and Shepard's inability to get him self out of the situation that she had created. It had overloaded, presumably due to their proximity to it; it didn't really make sense but he shrugged them of after chastising Williams' for her misconduct and figured that he would piece it all together in his report.

Captain Anderson had demanded a word in private with the commander and Shepard was relieved to be rid of the two women.

"Are we taking Gunnery Chief Williams back to Earth? Or are we meeting up with her new unit directly?" Shepard had inquired, he wanted her off the Normandy before she realised that she was on the most advanced star ship in the alliance fleet and took advantage of Anderson's better nature to get her self stationed with him.

"Actually, I figured we could use a soldier like her. She's been reassigned to the Normandy." Anderson's reply hit Shepard hard; this ship was doomed.

John took a deep breath and tried to hide his expression; "I understand, Captain."

"Speak freely; do you have a problem with Ashley?"

"With all due respect, she's reckless. We don't need renegades on our ship."

"Now, come on, Shepard. You need to lighten up. I've read the reports about you. All of your old COs say the same thing; you're too straight laced. You're never gonna' make Captain if you can't respect the passion that people like Williams bring to the table."

"I tried it that way, sir. Passion first, honour second. It got a lot of people killed."

"I won't patronise; I can't presume to know what Torfan did to you. But my point stands, I need someone like you on my ship but you have to respect my style as well."

John shook his head; that was never in doubt. "I do respect you, Captain. I won't question again."

"No. I want you to respect me because of my experience not my rank. Can you do that? Honestly?"

"No. I'm sorry, Captain. Rank is the only thing I value." Anderson didn't seem to have expected this response and seemed genuinely hurt by it.

The captain shook it from his mind. "That wasn't why I came here, anyway. I won't lie to you, Shepard. Things look bad. Nihilus is dead, the beacon was destroyed and Geth are invading. The council's going to want answers."

"I ready to take full responsibility for the mission's failure, sir."

"No, I'll stand behind you and your report, Commander. You're a damned hero in my books. That's not why I'm here. It's Saren, that other Turian. Saren's a spectre, one of the best; a living legend. But, if he's working with the Geth, it means he's gone rogue; a rogue spectre's trouble. Saren's dangerous, and he hates humans."

The man who'd killed Nihilus had been named by a survivor who witnessed the attack. It was suggested that this Saren was a friend of Nihilus' and that he'd 'shot him in cold blood'.

"I think he came for the beacon. He might, possibly, have taken an important piece from it." Shepard hoped it was this; it would give him a good explanation as to why he had managed to fail his mission in such a disastrous way.

"You were there just before the beacon self-destructed. Did you see anything? Any clue that might tell us what Saren was after?" Anderson replied, not really expected anything.

"Just before I lost consciousness, I had some sort of hallucination; I was being fed images of synthetics, possibly Geth, slaughtering people."

"We need to report this to the council."

"I don't think that's necessary, Captain."

Anderson quickly changed Shepard's mind, suggesting that the beacon might have been storing blueprints for some form of Prothean technology; weaponry or otherwise, and that if Saren took it then they couldn't omit any detail.

John felt the instant need to reassure his Captain. "We'll find some way to take him down."

Anderson reminded him that Saren was a special agent; they would need to prove his involvement in the attack on Eden Prime to the council before they could make a real move against him and his Geth, the synthetics that wiped out Williams' unit.

He followed Anderson out of the medical room and found himself face to face with Ashley Williams, the woman he loathed more than anyone else on the ship.

He tried to walk past her, as though he hadn't seen her but she initiated a conversation before he could escape. "Hey, Commander; after what happened to Jenkins, the crew could use some good news. They'll be glad to see you're okay."

Her tone gave off the same insolence that most the crew exuded; she'd fit right it.

"You don't seem best pleased. Do you have a problem with me, Chief?" John's own tone begged for an aggressive response.

"You questioned my competence through the entire mission."

"That's because you're incompetent. The Captain thinks you can aim a rifle well enough, that's why you're onboard. As far as I'm concerned, with Jenkins dying and you joining us, we've just traded one reckless idiot for another!"

This outburst caught the attention of a good number of other crew men; and they looked ready to rip the commander's head off. John tried to ward them off with a snarl but eventually decided to retreat to the crew's quarters.

Staff Lieutenant Alenko joined him after a few minutes.

"That was cold, commander."

John's hand trembled; even in Kaidan's soothing accent, the comment hit him with an almighty level of guilt. But not guilty over what he'd said, but guilt over whom it had upset. The Captain, the navigator and this staff lieutenant were the only men on the ship that could claim to enjoy John's respect and, as such, the thought that they might lose respect for him cut him deeply.

"I don't regret what I said, lieutenant…"

Kaidan was finding it hard to like the commander; he admired men that could play by the rules but he didn't admire men that used the rules to justify bullying other people. The commander cut his stream of thought short, however.

"…but I'm sorry that I said it, all the same. I didn't mean to upset you."

"It's not just me, commander. It's the crew as…"

John interrupted "I don't care; I don't respect their opinions and I don't need to."

How could he do that? Kaidan couldn't understand how the man that had spoken with such compassion just a few seconds before could revert to making repugnant comments like that so quickly.

"Permission to speak freely, sir."

John dreaded what was coming but willed it on, knowing that he probably deserved it "Granted."

"Did something happen to you? No one is that horrible on purpose."

That word, 'horrible'; it stung. John thought back to Mindoir and the slaver attack. Ever since the moment he had been rescued the military had meant everything to him; all of his emotions were catalogued and stored for military use only. Admiration was for his superiors, comradeship was for his officers, compassion was for his crew and love was for his ship. Anyone that didn't fit the standard military mould deserved nothing from him.

He couldn't tell anyone, so it didn't really matter. "Nothing happened to me. If I am… horrible, then it's because I choose to be."

The commander was lying and this made it worse than anything he could tell a stranger just because he asked him to.

"I don't believe that. But, if you ever need someone to talk to, I'll try to be there for you, commander."

Kaidan left before John could reply "Thanks."

He left for the bathroom. He stared into the mirror; he stared into his emerald green eyes and his jet black hair. His looked at his pompous moustache. He shaved it off. He looked at himself one final time; John Thomas Shepard, the Butcher of Torfan.


	3. Chapter 3

As the Normandy pulled into the Citadel and Alenko, Moreau and Williams admired the council's flagship, John sat on his bed fingering his ancestor's medal.

An Iron Cross, from a conflict in Earth's history; he couldn't recall which conflict nor which of his ancestors it had belonged to. Its only significance was as the last surviving piece of his family besides himself.

He had found it when his first CO had taken him to Mindoir; "Remember, Shepard. This is what you're fighting for. This is what slavers do, and remember that when any Batarian piece-of-shit begs for his life; pull the trigger and avenge your family!"

Major Kyle, the man commanding the raid on Torfan, wasn't nearly as ruthless but the seeds had already been planted in Shepard's mind.

Memories of Mindoir and Torfan cycled for his mind; seeing his father shot down before his eyes and then, eight years later, seeing the terrified look in the eyes of the men he shot down. They weren't men back then, they were monsters but as soon as he had completed his mission they became men and nothing anyone could say could lift the burden John carried with him.

The pilot alerted him that they had docked and he jumped to his feet. He beat his squad mates to the air lock by about ten minutes, having been wearing his combat gear long in advance. The others questioned the need for combat gear, they were hardly expecting a threat, but Shepard just followed the orders he was given and reminded them to do the same.

The human ambassador, Donnel Udina, had organised a meeting with the Citadel Council to being at the conclusion of their own investigation into Saren. Their initial meeting with the ambassador didn't go without a dressing down; Udina accused Shepard of failure and he, silently, accepted it.

Once Captain Anderson and the ambassador left, with orders for Shepard and his squad to follow them up to the council chamber a while later, Williams let a comment hang in the air.

"And that's why I hate politicians."

John thought, for a moment, that he could lead it but her tone infuriated him.

"You have a serious problem with authority, Williams."

"Oh, come on."

"No! If you've got something to say about someone that you can't say to their face then it is best left unspoken."

Ashley's chin trembled; Shepard was one of her heroes, the battle of Torfan was the stuff of legends, but the man she now answered to refused to live up to any of her expectations.

"I understand, sir; I try to keep quiet."

"Look, do you two want to make your own way to the chamber? I need some time on my own." He'd spent most of his time on the Normandy alone but he had always felt too close to the rest of the crew.

"Sure, Commander; come on Ash, we could check out the market." Alenko's voice was still soothing and was a pleasing contrast to Williams' but even the Lieutenant's presence was too much for Shepard.

The Commander went down to the lake outside the embassies and leaned one arm on the railing, holding his forehead with his freehand. His head throbbed, his eyes burned and his body ached.

He tried to take his mind off of all the things that were aggravating his migraine; a rouge for a captain, a boat-load of glorified pirates for a crew and the horrible feeling that an almighty shit-storm was about to hit the fan, by admiring his new armour.

It was Titan armour, class four, and the grey camouflage appealed to Shepard, it gave off clear signals; efficiency and purpose.

…

Alenko and Williams took the elevator up to the market and, after an awkward minute of silence, Williams was the first to speak.

"Hey, what did you and the Commander talk about when you were alone with him?"

"He's a stone cold military man, Ash. You must've met a few of them throughout the years. He says as little as possible and without an inkling of tact."

"I guess …I just didn't think a war hero could be like that …The 'vids' paint war heroes as rogues with hearts of gold."

Kaidan had had a peek at Shepard's heart but telling Ashley that he wasn't the mask that he showed her felt, somehow, like betraying him. "That's Captain Anderson. I think the brass picked Shepard for that very reason; we've got a rogue willing to take risks as our Captain but we've got a by-the-books type as our XO to make sure he doesn't take too big of a risk."

"But there's a difference between by-the-books and 'asshole'…"

"Wow, Ash the Commander's got issues but that doesn't make him anything less than your superior."

"Oh come on, Kaidan. People have to earn respect."

"Yes; and you know better than I do that Shepard earned all the respect he needs on Torfan."

Ashley couldn't fault his logic because, in truth, she felt exactly the same but she was compelled to defend her previous statement.

"You just stick up for him 'cause you're the only one he talks to like a human being."

The elevator ride came to an end and, whilst they went on to check out the market and came to the council chamber in jovial spirits, their conversation was neither renewed nor resolved after that.

…

John had just concluded a conversation with Garrus Vakarian, another Turian and the man responsible for investigating Saren, and Shepard had come to respect Vakarian; he was professional with a clear flare of honour that begged him to continue with his investigation even though it had just been closed by the Citadel Executor.

Garrus had bid him farewell with information on a possible lead.

"I've got some 'intel' that suggests Dr. Michel, the med clinic doctor, might have some important information."

"I'll check it out if I can; keep up the good work, agent."

Williams and Alenko emerged from the elevator and Shepard acknowledged them with a nod before continuing towards the council chamber.


	4. Chapter 4

"Well, that didn't work."

The Council had refused to acknowledge any evidence of Saren's involvement in the attack on Eden Prime, Saren himself (via link-up) had provoked the Commander into a hostile exchange of words and the Ambassador's petition to have Saren disbarred from the spectres had been denied.

"I have already got a lead, Captain; I should not waste time." John waited for his Captain's approval, with his chest already half turned to the direction of the elevator.

"Good, take Alenko and Williams with you."

"No, sir; they would slow me down."

Anderson wanted to challenge the Commander but he knew it would be futile and Shepard _was_ right; they couldn't afford to waste time. Instead, he made a mental note to chew the Commander out once he got back to the Normandy.

John had already taken off when Udina met up with them to offer the lieutenant and the gunnery chief an additional lead.

"I've got a contact in C-Sec, Harkin; he might know a think or two about Saren."

"It couldn't hurt to go talk to him…" Anderson concurred, but the exhausted tone in his voice suggested that it might do something just short of hurting them.

"…he'll be in Chora's Den."

Kaidan just gave a nod and the pair made their way to the bar.

After a few moments of silence in the elevator, Williams turned animatedly to the Lieutenant "Oh my God; I get it! You're attracted to him, that's why you act like he isn't an asshole!"

"Please; I am not that shallow." Alenko's tone was uncomfortable "Besides, I've already got my sights set on someone."

"That didn't sound like you."

"What didn't?"

"You just don't strike me as the…" she mimicked the Lieutenant's low, smooth voice "…'got my sights set on someone'…type."

Alenko just laughed, the tension was broken.

Once the elevator had stopped, they made their way into Chora's Den, passed two shady-looking Turians.

It wasn't hard to spot Harkin, a bald C-Sec officer, holding his glass casually whilst he ogled the plethora of Asari dancers placed all around the bar in tight full-body cat suits.

…

John had caught up with Garrus halfway to the Med Clinic and they were able to make an entertaining conversation.

"I just hate all this 'red tape'…" the Turian borrowed a human expression in declaring his loathing of C-Sec regulation.

The Commander agreed, finishing his sentence for him "…It shouldn't matter how you do your job, so long as you do it."

This caught Vakarian off-guard "Really, Commander? You made it sound like you loved regulations earlier."

"You're right. _I _love regulations; but regulations are for soldiers, not detectives."

"I'm not really sure I follow."

"My job is about taking lives, so the regulations need to be as tight as possible to stop me from taking any more lives than necessary because, as a soldier, if I could; I would. But you, you're job is about saving lives, so the regulations need to be as _loose _as possible to make damn sure you can save as many lives as possible."

"Now, I get it. So, I guess, you're not a fan of the spectres?"

Before the Commander could answer, however, they encountered the Med Clinic door; it was locked. They inferred that Saren's agents might have got to the doctor before them.

They took positions at both sides of the door, the Turian crouched to the floor and, in one fluid motion; the Commander overrode the door's controls and made his way in with his hands up as Vakarian slipped, unseen, over to behind a table.

Their previous suspicions were confirmed and one of the thugs held the doctor at gun-point.

"Who the hell are you?" The thug retrained his gun onto the Commander, he gave a quick nod to Garrus, and the Turian popped up from cover and blew the man's brain all over the floor.

Before the first body hit the ground, John took his own pistol and fired a single cryo-round into the second man's chest. As his heart froze, the Commander made his way over the table and delivered a powerful blow to his chest; his heart exploded and the blood soaked Shepard's helmet and the bottom half of his jaw.

He turned to the third thug, Garrus took out the fourth, and he said, holstering his pistol "Drop it…"

The third man dropped his own pistol almost the second those words left John's lips.

"What is your name?"

"B…Brian, my name's Brian." He had already fallen to the floor, starring in shock at his dead comrades.

"Well, Brian; I have some questions. First were you going to hurt this civilian?"

"No, No; we was jus' gonna' scare her."

"That's good. Anyone who knows me knows that there are two things that I cannot stand. The first one is hurting civilians…"

Brian interrupted "O…Okay, man. What's the next question?"

"I wasn't finished!"

Brian's eyes began to well up.

"The second thing, that I cannot stand, is: lying."

"I'm not lying, man. I'm not lying…"

"Shut up!"

Brian just nodded.

"Now, when it comes to people who hurt civilians, I break their trigger finger. But, when it comes to people who lie…" his tone started to become maniacal and he wiped the blood off of his mouth but held his finger their before turning to the terrified thug "…hold out your tongue."

"Oh, God." He started to wet himself.

John slapped him hard in the face "Now, you have ten seconds to tell me exactly what I want to know, or I'll cut your tongue off!"

Brian strung out his next few sentences into a wild stream of consciousness and John picked the most important parts out of it.

The thugs worked for a local gang leader, Fist, and they were send to make sure that the doctor, Dr. Michel, wouldn't tell anyone one about a Quarian that had come to Fist with sensitive information about one, as John and Garrus inferred without the thug's help, Saren Arterius that she was willing to trade in return for safe passage.

…

Harkin had made one too many vulgar remarks about Williams and Alenko had thrown him out of the bar. He hadn't offered them any useful information and the Lieutenant decided to take advantage of their uselessness.

"I'm sure the Commander has got it under control. So, would you like a drink?"

"Real subtle, Alenko; but sure, I wouldn't mind."

"It's Kaidan, please."

Ashley offered him a smile and took her helmet off. She was beautiful.

Their eyes met and they held the gaze for one second too long. Kaidan shook his head and motioned to the bar. "What're you having?"

"What're _you _having?"

"Beer; is that good?"

"Ugh."

They laughed, too distracted to notice most of the people around them being quietly ushered out of the bar.

…

Fist's office, so Dr. Michel informed them, was located in a bar called Chora's Den. Shepard and Vakarian flew into action, they marched as though every second between them and Fist took year of their lives.

Between breaths, Vakarian asked the Commander "Gonna' pull that sociopath act on Fist?"

"No; it only works on low-level goons."

"Ha!"

They found their way to Chora's Den in next to no time at all and were met by two angry Turians.

…

As soon as she heard the fire-fight outside, Chief Williams, plucky as ever, charged out of the bar.

Kaidan finished his drink with a large gulp, nearly choking, slammed it on the bar and grabbed Ashley's helmet as quickly as he could before he made off to follow her. But he encountered a thug scrambling to lock the door and another knocked him to the floor.

He made to grab his weapon but yet another thug rammed him up against a wall, beating him senseless.

"Williams! Where's your helmet?" The commander shouted, after they had done away with their would-be assassins.

She didn't answer. Instead, she panicked, trying desperately to get the door open. "The lieutenant's still in there!"

The commander demanded that Ash "Move!" as adrenaline kicked in and, just as the chief got out of range, John through a high explosive at the door, blowing the metal panels to pieces and killing a few thugs immediately.

He rushed past Williams and straight into a hailstorm of gun-fire. He took a nasty shot to the shoulder before he could get away with the lieutenant's limp body in tow.

"Vakarian, Williams, you two take it from here!"

The responses "Yes, sir!" and "On it!" came simultaneously.

John bound to the Med Clinic, with Kaidan slumped over his good shoulder, more than ready to pass out once he got there.


	5. Chapter 5

**A/N: Apologies for the delay. This is a short one, I should have a better idea of what I'll be doing and when until summer by next week.**

…

Kaidan, along with the even more badly injured Quarian that Garrus and Ashley had managed to recover, had been transferred to the Normandy; lest any of Saren's agents decide to finish what Fist's agents started.

John hadn't left Kaidan's side. Apart from to put on his dress uniform, his bandages went too far up his neck for him to dare expose it by wearing his duty uniform.

"I don't think she's going to make it." Chakwas chimed in, seemingly as though the Commander needed any more stress.

But he replied with the same coldness that had surrounded him since he was sixteen. "Have you found anything useful on her Omni-tool?"

"I think so. But…"

Williams' entrance broke the doctor's chain of thought.

"Commander, could we talk?"

Shepard had been dreading this but she deserved a chance to explain herself. "Fine. Doctor, give us some privacy."

"I really should stay with the Quarian."

John didn't need this; people should just do as they were told. "You said she was as good as dead, yourself. She is no need of your immediate attention. I am ordering you to leave."

Chakwas gave half a scowl; this aged the grey-haired woman even further. She left at as slow a pace she could manage.

"So, chief; this is the part where you tell me just what the _hell_ happened."

"It was my fault, Commander. I offered Kaidan a drink, we stayed longer than we should have and, when I heard gunfire, I rushed out. He must've stayed back to get my helmet."

John got up from his seat, with ever intention of towering over his subordinate. "First and foremost; never use an officer's first name when you're speaking to me!"

"Sorry, Commander." The weak response came from Ashley's mouth like a foreign dialect; forced and undignified.

"Second, never shirk your duty; I shouldn't think that I'd need to explain that one to you."

The same response met the Commander's ears.

"Now, as for the alcohol and the attempted fraternization, I don't care how you waste your time but don't try to drag a fine young officer like the Lieutenant down with you… Am I clear?"

"Yes, sir; we're clear." She had to fight harder than she ever had before to stop herself from correcting the Commander's mistaken interpretation of the man that now lay bloodied and bruised in the medical bay.

"Dismissed… Oh, and if you _ever_ run into a fire fight without your helmet again.., I'll shoot you my self."

"Oh, okay, Commander… I… I actually want to see the Lieutenant." Ashley made to step past Shepard, but he blocked her path.

"Do really think he'd want to see _you_, when he wakes up?"

A third voice answered. "I would."

"You're awake." John whispered as he turned to the Lieutenant, Alenko had since propped himself up and revealed the bruises all over his bare chest.

"Commander, I offered the Chief a drink. She wouldn't have taken her helmet off if I hadn't allowed her to let her guard down."

John wondered how much of their conversation he'd heard and decided to err on the side of caution. "There is no need to take the fall for this, Lieutenant. Chief Williams has owned up and accepted the blame." All John really cared about was hearing that voice again, the voice that had been taken from him.

"Bullshit! This isn't her fault. And it isn't mine, either. If you'd have taken us along with you then none of this would've happened."

John couldn't think of a response, he couldn't bare the harsh words and he stood silent and trembling for a moment. He tried to gather himself "Chief, get out!" and he pushed Williams out of the door, sealing it behind her.

"Sir, I don't care what you say; you were out of order!"

John just stood there, his eyes full of hurt and his chin trembling.

Kaidan couldn't stop; he was full of rage that begged to be let out. "What the fuck is this? If I was anyone else you'd be jumping down my throat right now."

"Kaidan, please…"

"What is wrong with you?"

John fell; he caught the desk and shifted his eyes away from the Lieutenant; this surreal motion generated a near unbreakable tension between them and for what felt like an eternity neither dared to speak.

Kaidan felt a horrible sensation overwhelm him, his Commander; a ruthless bastard in every sense of the term, had just crumbled under the pressure of a few harsh words from a man he hardly knew. "Sir.., you're unstable. I think you need help."

Almost immediately a deafening scream filled the Lieutenant's ears "No!" and it drew the attention of everyone gathered on the crew deck. They stared into the medical bay just as the Commander regained his stance.

"You're out of line, Lieutenant! Now, I risked my ass getting you out of a certain death situation, you will accept my version of events because I am your superior officer! The Chief screwed up, you got caught, and I got you out! Do I make myself clear?"

Kaidan didn't know whether to be shocked, scared or elated but he quickly settled on a hideous mixture of the first two. "Yes, sir; perfectly clear, sir!"

John just nodded, tugged his shirt back into to place and made for the door.

He flew into the restroom and keeled over the toilet; his migraine lit a fire behind his eyes and he choked on the blood that had forced its way when his stomach tired to get rid of his non-existent breakfast.

It was never going to end; good people died, bad people lived. Shepard had been so afraid that he'd lost a good officer and, yet, the moment his prayers were answered the Lieutenant had turned on him like everyone he had ever saved.

The knowledge that it had been the commander's fault made it easier for the Chief to talk to Kaidan whilst the Quarian on the next bed lay there, slowly dying.

"You stuck up for me."

"I don't like bullies."

Ashley tried to put her feelings into words but she'd never been very good at it "Well, it's good to know you'll be okay."

"Maybe we should leave the drinks for shore leave."

"Is that an offer?"

"I don't care what the commander says. I enjoy your company, Ash."

His words, so smooth and fluent, put Ashley at ease. She smiled.


	6. Chapter 6

**Author's Note: After the Extended Cut debacle I found the plans for my story ruined and, because of this, I have had to do an extensive re-working of the plot. It is still a story that I am desperate to tell and I have tied it in with the original themes of my old story plan. If, however, you think that the change in tone from this point onward is too drastic, please feel free to tell me. I am not particularly proud of this chapter but it needs to be there. **

**Anyway, thanks for the feedback and on with the show.**

…

"I don't think Shepard's ready for this.

"It doesn't matter, Captain; we might not get a _third _chance."

"Alright…but we need to keep an eye on him."

Hours of data mining had produced a single important file on the dead Quarian's Omni-tool; a recording of some incriminating dialogue between Saren and an Asari Matriarch named Benezia.

All the necessary authenticity checks had been run; the Omni-tool had been sent away for a more in-depth analysis, and, with Saren linked to the Geth attack on Eden Prime, the council had rescinded the Turian agent's spectre status.

The council was, however, reluctant to commit military resources in tracking the now rogue Saren and his Geth army. With this in mind, and with Udina's own political motivation trickling into it, a compromise had been struck; Shepard would be granted spectre status and his own ship in order to use whatever means necessary to bring the traitor to justice.

What should have been a great honour felt more like a political handout and Shepard's response ("I am deeply honoured.") would have seemed false if it didn't fit in perfectly with the rest of the monotony that pervaded his overall tone.

Garrus congratulated the Commander, relieving Williams of that duty, "You'll make a fine spectre."

"I could use you on my ship, Vakarian. You know more about Saren than me and you're an outstanding detective."

The crisp Turian voice replied immediately "I'm onboard…"

Udina interjected "Commander, I've _discussed_ it with Captain Anderson and we've come to a conclusion about your ship."

John was sure that a spectre should choose his own ship but he was grateful for any kind of direction. "Sir?"

"The Normandy, she's yours now." Anderson's own voice seemed dejected.

"I'll take good care of her."

A weak hand-shake and a forced smile sealed the deal.

"We don't have any time to waste. Do we have any leads?"

"I'll patch them through to the Normandy. For now, I suggest visiting the Artemis Tau cluster and trying to track down Liara T'Soni; she could have incredibly valuable information, she's a Prothean expert and, more importantly, she's the daughter of Matriarch Benezia."

With nothing more than a nod to Udina and a salute to his former Captain, Shepard made his way back to the Normandy, _his_ Normandy.

As soon as the Commander was on the ship, the pilot offered up his console; "Got anything you wanna' say to the crew?"

John leaned over the console and spoke to his sub-standard crew on his state-of-the-art ship.

"Attention, this is your captain speaking. I have replaced Captain Anderson but our mission remains; we are to track down the rogue spectre, known as Saren Arterius, responsible for the deaths of Corporal Jenkins and Agent Nihilus, both men who relied on this vessel to protect them, and numerous colonists on Eden Prime. I have no doubt in my ability to bring this murderer to justice and I give you my word; we will avenge those deaths if it's the last thing we do!"

With that the Normandy thundered towards the nearest mass relay and on to the Artemis Tau cluster.

Shepard had yet to receive the proper authorisation necessary to bring Agent Vakarian along on missions and, therefore, had to, begrudgingly, bring the two most combat-experienced members of his crew along; Alenko and Williams.

The Commander ability to operate the Mako, the Normandy's on board land vehicle, was an annoying metaphor for the tension between himself and his squad mates; the Mako responded to his orders in a clumsy delayed fashion and his patience was wearing evermore thin.

As they drove along the jagged rocky paths of the volcanic world of Therum, a Geth Ship appeared to beat them to their target and blocked their route with two Geth Armatures, vicious anti-tank versions of Geth soldiers.

Rather than ordering one of his squad mates to man the gun, Shepard simply stopped the Mako, switched to the gun and ripped them to shreds; pouring all of his built up anger out onto the metallic soulless punching bags before him.

After that, Williams seemed to take the hint and went up to the gun for the remainder of the journey. With Williams on the gun, Shepard at the helm and Alenko manning the scanner; each squad member performing a duty that left little room for banter, the silence, whilst still their, lost a lot of its awkward weight.

As they came closer to Liara T'Soni's facility the path became narrower and narrower until a particularly steep hill laden with boulders forced them to abandon the Mako and run along on foot.

"After this mission, I'm getting you both Titan armour." Shepard told his squad as he noticed their frequent need for cover.

"I like my own armour, Commander." Williams responded, she lightened up the remark with a softer tone than wouldn't otherwise be necessary with any other officer.

"I like my briefs, Chief. That doesn't mean I want to run around shooting Geth half naked."

"Shame." The Lieutenant interjected.

This was met with the slightest half-laugh half-cough from the Commander and Ash and Kaiden offered each other confused glances.

Sure enough, some Geth noticed the Gunnery Chief was distracted and a flurry of shots came storming towards her. Shepard immediately sprang into action, he pushed Williams down hard and stood, in her place, with no time to stop the shots from carrying his left shoulder, and thereby his body, off a few metres.

Shepard refused to be kept down for long, however, and he fired precise shot after precise shot at the enemy soldiers; neutralising all of them just before his shields over loaded.

A few small-scale battles later and they entered the facility, with Shepard's shoulder still throbbing and the new sense of uneasiness and discomfort hanging over the squad.

"You alright?" Kaiden asked Ashley, touching her arm.

"Yeah… Get off." She replied shrugging him off and marching to catch up with their Commander.

Shepard stood with cold disinterest, picking off his enemies and suppressing his rifle's recoil as best he could. He found fighting Geth much easier, like target practise; there were no screams of pain, no sobs, no nicknames, there was no banter or any other sense of humanity.

John didn't have to stay behind cover, hiding his tears, as enemies screamed proclamations of revenge before being violently removed from the universe.

Leaning over a thin metal railing he fired short burst after short burst, Geth soldiers fell one after another; their lights went dim and their bodies went limb.

After all the Geth had fallen, Shepard was left with an angry looking Krogan; it looked almost as inhuman as the Geth and it would rather die than express genuine emotion.

Shepard leapt down from the railing, as Williams and Alenko sent down a rain of bullets over the Krogan, and he threw three frag grenades, one after the other in quick succession, forcing it down onto its knees but, before he could interrogate it, Williams sent off her last bullet right through its brain.

He didn't let this bother him; he'd get his answers from T'Soni.

One mining laser, two explosions and a daring escape later brought T'Soni onboard and questions were answered.

Not only did Liara make it clear that she was not Shepard's enemy, she also showed him some genuine admiration that he found lacking in the rest of his crew.

"You were touched by working Prothean technology… that would have destroyed a lesser mind… you must be remarkably strong willed, Commander."

Later, as he admired his new quarters, Shepard's rest was interrupted by a young Kaidan Alenko.

"Come in."

"Commander…"

"Please, sit."

"Commander, I don't really know what to say; you saved Ashley's life today, I don't know what I am supposed to make of that." Kaidan's words didn't fit with his tone; he sounded as though he spent hours thinking it over and yet he had nothing better to say than that.

"You don't have to make anything of it, Lieutenant. I am this Ship's Captain, now, and that comes with a responsibility that I do _not_ take lightly; everything I do is designed to ensure the safety of my crew."

"No, see, I don't buy that. Ash wants to thank you but if you're going to shrug this off, then why should she bother?"

"Alenko, sent her in; I need to settle this."

Williams walked in immediately, having been at the door listening. Shepard shooed the lieutenant away with a salute and returned to his chair.

"Commander, I have to thank you…"

"Shut up." This caught the chief off-guard and a look of deep resentment filled her face, her lip twitched with ever passing second. "You do not need to thank me for doing my job! My saving your life was not a personal kindness. You let that Quarian girl die because you were incompetent, not because you were malicious."

Williams moved to speak but Shepard cut her off "Ah…"

"Now, the same applies here; I saved your life because I am competent not because I am compassionate. If you want my compassion, you have to earn it. I wish I could boot you off my ship right now, but between you, the doctor, the pilot and most of the crew I can't get enough men to replace you. So, this is how I am going to play it…" he extended his hand across his desk "a clean slate, for you, you can still hate my guts but I'll try act as though we've only just met, in return; you'll work hard to prove that you deserve to be on this ship, deal?"

Ashley furrowed her brow, contemplating, leaving the Commander hanging for a good five seconds before taking his hand with an aggressive grip "Deal!"

"Good, sent the lieutenant back in."

"Yes, sir; will do."

Just before she left, Ashley caught sight of an old fashioned hard-cover black book with a gold engraved title. "Is that bible?"

"Leave."

With that, Ashley left and, a few hushed words later, Kaidan entered.

John raised his hand to stop Kaidan from speaking.

"Lieutenant, I know enough about command and enough about the importance of this mission to know that my officers need to be able to trust me. I'm on good terms with Pressly but I can't just leave crew morale up to my XO. What can I do to start repairing the damage I've done to our relationship?"

"Off the record, Commander?"

Shepard responded with the slightest of nods.

"See a psychologist."

"Done." John offered the lieutenant his hand.

Kaidan wavered; the comment had had none of the impact it should have had, but he took the hand and the promise of a better relationship with his Commander, nonetheless.


	7. Chapter 7

Chakwas was sat in the medical bay, alone, at her desk. After the Quarian's body had been taken away, very few crewmen wanted to complain to the doctor about stubbing their toe, drinking some bad soup or pulling a muscle.

Shepard moved past the beds with a nod to the doctor, that she didn't acknowledge, and entered the small room that Liara T'Soni had claimed as her own.

"Have you come to check up on me?"

With anyone else, Shepard could imagine that question infused with annoyance but the young Asari spoke with a child-like innocence.

"No. I have a few questions that I need answered."

Liara appeared to hesitate, furrowing her brow, before she responded.

"I am happy to answer them." Before she could add anything more, Shepard cut her off.

"Good. I've just received my new assignment from Ambassador Udina; your mother has been spotted on Noveria. I am going to arrest her. I need to know that you won't try to stop me."

"Commander, I…"

"Good."

Another furrowed brow begged the question.

"I can see you're conflicted. So; I have my answer. You will not be accompanying me."

"I suppose that is best."

…

"Why do you always make excuses for him?" Ashley's tone threatened to rip Kaidan's answer from his mouth.

"I am not making excuses. I'm just saying; maybe you two just got off on the wrong foot."

"Or maybe he's just a dick." The hearty laugh, that followed, softened the comment.

Kaidan didn't join in; he just traced her smile with his eyes and if she noticed it she didn't say anything.

…

"You watch you're tongue, crewman!" Pressly had no time for insolence. For what it was worth, he liked the Commander.

"Sorry, sir." This particular crewman immediately dipped his head down and lunged straight for the table and the safety of his cohorts.

…

Admiral Mikhailovich was waiting for the Commander form the moment the Normandy docked.

He called it an inspection. Shepard saluted. He criticised the assignment. Shepard apologised. He criticised the design. Shepard accepted it. He criticised the crew. Shepard hid his fear behind quick apologies and minimalist responses.

Shepard had sent Alenko and Williams off on their own; the latter came back with a new supplemental mission and the former returned with the ship's new 'morale officer'.

As soon as this Lieutenant Russell found his way to the Commander, Kaidan leapt into the Normandy, refusing to make any eye contact with his captain.

The handshake revealed a confident man with hidden fear and another confident man with only the pretence of nervousness and fear.

At least this man was willing to engage in the pretence even when no-one else was with the two of them.

The introduction was little more than both of them barking rehearsed lines at each other.

"Mr. Moreau, take us to Noveria; Udina stressed haste, there's no telling how long the Matriarch will be there."

"Sure thing, Commander…" The pilot added, in a whisper "…'cause I usually just go at half-speed."

Shepard let it slide, with far too much on his mind to care about yet more insolence.

The Normandy docked as the Noveria authorities made a promise to check Shepard's "identification" before he would be allowed entry.

As they began their approach to the facility's entrance, Williams spotted a heavily armed security unit seemingly ready to greet them. "Sir, we might have a problem."

"No, I they're the ones with the problem. Nothing is stopping me from completing this mission." Shepard's word felt loaded with contempt.

Fortunately, the security guards were told to stand down seconds before Shepard would've shot each and every one of them between the eyes.

His meeting with Noveria's Administrator went as expected and a few insults and one death threat later Shepard had the Matriarch's whereabouts and a key to access the route to her.

As they journeyed to Peak 15, the Matriarch's research facility, they found their path littered with Geth. Shepard's demand that they take time to hunt down and destroy each and every one of them left their car on its last life by the time they reached the facility.

The team worked as fluidly as they could; every order Shepard gave to Alenko was met with a delayed response, but it never affected their effectiveness.

Once they reached an area patrolled by a small contingent of Geth and once they had taken them down, they got their first glimpse of what the Matriarch had been working on.

Two hideous monsters, with vicious whipping tentacles hovering above their mantis-like heads, smashed their way out of the drain covers on the floor. The first one lunged for Kaidan, tackling him down to the floor.

Before it could pierce his helmet with its snapping pincers, Shepard instinctively dropped his gun and leapt at the monster. He beat on it with blow after blow driving its head further and further into the wall until it burst, spraying acid all over him.

Williams unleashed a sustained volley of fire on the second; overheating her rifle and punching a gaping hole through the creature's abdomen.

Williams handed Shepard his rifle as he marched off, trying to wipe the acid from his armour. "Good job, Chief; we'll have to be careful from here on."

From then one it was a silent and cautious walk through the facility. They encountered some trouble, having to re-initialise a Tram-system to reach the Matriarch and cull a few more of the hideous creatures but their journey remained relatively uneventful for a good half an hour as each of them mulled over the others' character in their mind. They all came to the same conclusion of one another: "I'll have to wait and see."

They met up with a small contingent of mostly humans and Turians trying to handle what had clearly been an outbreak of the monsters and Shepard instantly came to respect its Commander as an upstanding and necessarily (and refreshingly) stern officer. The man directed the trio to the outbreak's source and what culminated in genocide of the "Rachni" as they were being called.

As they made their way back from that and onto the final showdown, however, they were blocked on their path by the same contingent that fought alongside just recently.

The soldiers seemed to raise their guns prompting Alenko and Williams to take up a defensive position. Shepard, however, walked towards the Captain without any weapon drawn.

He assessed the situation. "Stand down, Captain."

"I'm sorry, Commander; Benezia's orders…"

"I said: Stand down!"

At this, and to Shepard's complete astonishment, the Captain raised his gun.

Kaiden exclaimed "Shepard!" before running to his side and tackling him to the ground. Not much later the fire-fight began and Shepard picked himself off the ground, taking shot after shot and showing no reaction.

The Captain paid for this in blood, along with the rest of his men on the way to their target.

Desperate to make up for his previous failure, Shepard dove straight into offense once they encountered the Matriarch. "Williams secure the far-side, Alenko take the left."

Shepard himself dropped the first set of Asari commandos, weaving through and dodging the Matriarch's biotic volleys. He overwhelmed Benezia, delivering a brutal right hook and pinning her to the ground. As Shepard arrested her, Williams made short work of her bodyguard and the assorted waves of Geth that attempted rescues with uncharacteristic desperation.

Shepard dragged the groggy Matriarch to her feet and the tank in the centre of the room burst into life. The Rachni "Queen" thrashed around in her cage. She smashed her mouth against the tank, her squelching jaws pulsated as if trying to speak and she seemed to tele-kinetically drag a fallen bodyguard up to her tank before talk through it.

The dead Asari, as if translating the Queen's words, spoke of her plight and the ultimatum Shepard now face. The Queen rejected her children, whom Benezia had been trying to raise as an army for Agent Arterius. She also presented the Commander with a choice, framed with a bias of course; "Will you release us?"

Releasing the Rachni meant a potential ally but an equally likely distraction from Saren if her children were anything to go on as to the temperament of Rachni. Killing the Rachni would mean extinction for the Rachni but an end to any serious threat other than Saren.

Williams, who had by now joined the Commander, demanded execution and Shepard was inclined to agree. Kaidan, however, raised an objection.

"You can't doom an entire species for the sins of its past."

He was wrong; John _could_ do just that. Perhaps, however, the tone in his voice or the emotion in his eyes changed the Commander's mind. The coin was tossed and Williams weighed the coin to just even with Shepard unsure.

The Commander gave them both a quick glance, he squinted his eyes as if to make a better estimation of their sincerity.

He chose Kaidan… and the Queen went free.

All that was left was to take their prison away for a… conversation.


End file.
